Difference between revisions of "2010 Summer Project Week"

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__NOTOC__
 
__NOTOC__
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Back to [[Events]]
  
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Back to [[Project Events]], [[Events]]
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[[image:PW-MIT2010.png|300px]]
  
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[[Image:PW-MIT2010.png|300px]]
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=Welcome to the web page for the 11th Project Week!=
 +
==Summary==
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The 11th PROJECT WEEK was held on June 21-25, 2010 in Boston, at MIT and Brigham and Women's Hospital. It recorded 126 registered attendees, who worked on 71 projects. These attendees represented 30 academic sites and 15 companies. Participants traveled to the project week from 9 countries (Austria, Singapore, France, Germany, Japan, Italy, England, Poland, and Canada), and from 16 states within the US (MA, NY, NC, MD, CA, UT, OH, MO, GA, PA, CO, IA, FL, DC, CT, NM). The projects, agenda, and affiliations of attendees are detailed below.
  
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A [[Project_Events#Past_Project_Weeks|summary]] of all past Project Events.
  
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==Background==
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<gallery perrow="3" widths="200px">
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Image:2010_Summer_Project_Week_Group.JPG|Volume Rendering Breakout Session
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Image:2010_Summer_Project_Week_Group_2.jpg|Raise Your Hand if you are a NRRD
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Image:2010_Summer_Project_Week_Group_3.jpg| Hard at Work
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Image:2010_Summer_Project_Week_Group_4.jpg| Brainlab VVlink OpenIGTLink Demo
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Image:2010_Summer_Project_Week_Group_5.jpg| Tutorial Contest Presentation
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</gallery>
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[http://www.smugmug.com/gallery/12687574_DsJjF '''More Photos ''']
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==Projects==
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=== Segmentation ===
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#[[2010_Summer_Project_Week_Robust_Statistics_Segmenter_Slicer_Module|Robust Statistics Segmenter Slicer Module]] (Yi Gao, Allen Tannenbaum, Ron Kikinis)
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#[[2010_Summer_Project_Week_Multi_scale_Shape_Based_Segmentation_for_the_Hippocampus|Multi-scale Shape Based Segmentation for the Hippocampus]] (Yi Gao, Allen Tannenbaum)
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#[[2010_Summer_Project_Week_Prostate_MRI_Segmentation|Prostate Segmentation from MRI]] (Andriy Fedorov, Yi Gao)
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#[[2010_Summer_Project_Week_SegmentationMeshEmbeddedContours|Segmentation on Mesh Surfaces Using Geometric Information]] (Peter Karasev, Karol Chudy, Allen Tannenbaum, GT; Ron Kikinis, BWH)
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#[[2010_Summer_Project_Week_SPECTRE|SPECTRE: Skull Stripping Integration with Slicer]] (Nicole Aucoin, Min Chen)
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#[[2010_Summer_Project_Week_White Matter Lesion segmentation|White Matter Lesion Segmentation]] (Minjeong Kim, Xiaodong Tao, Jim Miller, Dinggang Shen)
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#[[2010_Summer_Project_Week_EMSegmentation_kmeans|EMSegmentation: Automatic Intensity Initialization using KMeans]] (Priya Srinivasan, Daniel Haehn, Kilian Pohl, Sylvain Bouix)
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#[[2010_Summer_Project_Week_Left ventricular scar segmentation| LV Scar Segmentation Display and Fusion]] (Dana C. Peters, Felix Liu, BIDMC, Boston)
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#[[2010_Summer_Project_Week/The Vascular Modeling Toolkit in 3D Slicer|The Vascular Modeling Toolkit in 3D Slicer]] (Daniel Haehn, Luca Antiga, Kilian Pohl, Johannes Schick, Steve Pieper, Ron Kikinis)
 +
 
 +
=== Registration ===
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#[[2010_Summer_Project_Week_RegistrationCaseLibrary|The 3DSlicer Registration Case Library]] (Dominik Meier)
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#[[2010_Summer_Project_Week_RegistrationEvaluation|Evaluation of Registration in Slicer]] (James Fishbaugh, Guido Gerig, Domink Meier)
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#[[2010_Summer_Project_Week_HAMMER: Deformable Registration|HAMMER: Deformable Registration]] (Guorong Wu, Xiaodong Tao, Jim Miller, Dinggang Shen)
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#[[2010_Summer_Project_Week_Best_Regularization_Term_for_Demons_Registration_Algorithm|Best Regularization Term for Demons Registration Algorithm]] (Rui Li, Greg Sharp)
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#[[2010_Summer_Project_Week_Fiducial_Deformable_Registration|Fiducial-based Deformable Image Registration]] (Nadya Shusharina, Greg Sharp)
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#[[2010_Summer_Project_Week_MR_to_Ultrasound_Registration_Methodology|MR to Ultrasound Registration Methodology]] (Dieter Hahn, William Wells, Joachim Hornegger, Tina Kapur, Stephen Aylward, Andriy Fedorov)
 +
#[[2010_Summer_Project_Week_Groupwise_Registration|Groupwise Registration]] (Ryan Eckbo, Sylvain Bouix, Jim Miller, Hans Johnson, Kilian Pohl, Daniel Haehn)
  
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We are pleased to announce the 11th PROJECT WEEK of hands-on research and development activity for applications in Image-Guided Therapy, Neuroscience, and several additional areas of biomedical research that enable personalized medicine. Participants will engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, medical imaging sequence development, tracking experiments, and clinical application. The main goal of this event is to move forward the translational research deliverables of the sponsoring centers and their collaborators. Active and potential collaborators are encouraged and welcome to attend this event. This event will be set up to maximize informal interaction between participants. 
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=== Shape Analysis ===
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#[[2010_Summer_Project_Week_Shape_Test_Bench|Shape Test Bench]] (Marc Niethammer, Sylvain Bouix)
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#[[2010_Summer_Project_Week_Shape|Median Shape by Boundary-based Distance ]](Tammy Riklin Raviv, Sylvain Bouix)
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# [[2010_Summer_Project_Week_Shape_Analysis_UNC|Shape Analysis Projects, Integration with Slicer3]] (Beatriz Paniagua, Martin Styner)
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# [[Particle Based Shape Regression]] (Manasi Datar, Joshua Cates, P. Thomas Fletcher, Sylvain Gouttard, Guido Gerig, Ross Whitaker)
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#[[Automatic SPHARM Shape Analysis in 3D Slicer]] (Corentin Hamel, Clement Vachet, Beatriz Paniagua, Nicolas Augier, Martin Styner)
  
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Active preparation begins on Thursday, April 15th at 3pm ET, with a kick-off teleconference.  Invitations to this call will be sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties who have expressed an interest in working with these centers. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient coverage for all. Subsequent teleconferences will allow for more focused discussions on individual projects and allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading upto the meeting, all project teams will be asked to fill in a template page on this wiki that describes the objectives and plan of their projects. 
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=== Diffusion ===
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#[[NAMIC Tools Suite for DTI analysis|NAMIC Tools Suite for DTI Analysis]] (Hans Johnson, Joy Matsui, Vincent Magnotta, Sylvain Gouttard)
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#[[2010_Summer_Project_Two_Tensor|Implementing Two-tensor Tractography in Slicer (Python) ]](Stefan Leinhard, James Malcolm, Demian Wasserman, C-F Westin, Yogesh Rathi)
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#[[Efficient Diffusion Connectivity via Multi­directional F­star]] (Alexis Boucharin, Clement Vachet, Yundi Shi, Mar Sanchez, Martin Styner)
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#[[2010_Summer_Project_Week_Diffusion|Fluid Mechanics Based Tractography ]](Nathan Hageman)
 +
#[[2010_Summer_Project_QSpace_Reconstruction_for_Diffusion_Spectrum_Imaging_Data|QSpace Imaging Reconstruction for Diffusion Spectrum Imaging Data]] (Sudhir Pathak)
  
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The event itself will start off with a short presentation by each project team, driven using their previously created description, and will help all participants get acquainted with others who are doing similar work. In the rest of the week, about half the time will be spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half will be spent in project teams, doing hands-on project work. The hands-on activities will be done in 30-50 small teams of size 2-4, each with a mix of multi-disciplinary expertise. To facilitate this work, a large room at MIT will be setup with several tables, with internet and power access, and each computer software development based team will gather on a table with their individual laptops, connect to the internet to download their software and data, and be able to work on their projects.  Teams working on projects that require the use of medical devices will proceed to Brigham and Women's Hospital and carry out their experiments there. On the last day of the event, a closing presentation session will be held in which each project team will present a summary of what they accomplished during the week.
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=== IGT ===
 +
#[[2010_Summer_Project_Week_MR_to_CT_Registration_for_Prostate_Brachytherapy_Dose_Calculation|MR to CT Registration for Prostate Brachytherapy Dose Calculation]] (Andriy Fedorov, Dominik Meier, Hans Johnson)
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#[[2010_Summer_Project_Week_Intraoperative_Brain_Shift_Monitoring_Using_Shear_Mode_Transcranial_Ultrasound|Intraoprative Brain Shift Monitoring using Shear Mode Transcranial Ultrasound]] (Jason White, Steve Pieper, Junichi Tokuda, Pratik Patel?)
 +
#[[2010_Summer_Project_Week_Prostate_Intervention|Prostate Intervention(Junichi Tokuda,  Tamas Ungi, Haiying Liu, Sam Song)]]
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#[[2010_Summer_Project_Week_Liver_Ablation|Liver Ablation (Haiying Liu, Noby Hata)]]
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# [[2010_Summer_Project_Week_BrainLab_Aurora_Hybrid_Navigation|BrainLab-Aurora Hybrid Navigation]] (Isaiah Norton, Dan Marcus, Noby Hata)
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# [[2010_Summer_Project_Week_PerkStationModule|PerkStation Module]] (Tamas Ungi, Xiaodong Tao)
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#[[2010_Summer_Project_Week_Co-registration_of_PET_and_DWI_Images_for_the_targeting_of_Glioma_Biopsies|Co-registration of PET and DWI Images for Targeting Glioma Biopsies]] (Gareth Smith, Dominik Meir, Vince Magnotta)
 +
#[[2010_Summer_Project_Week_Implementing_Open_IGT_Link_to_Virtual_Place_for_research_support|Implementing Open IGT Link to Virtual Place for Research Support]] (Nicholas Herlambang, Masakatsu Hoashi, Junichi Tokuda, Noby Hata)
 +
#[[2010_Summer_Project_Week_Tracking_Neuroendoscope_Using_EM_Tracker_and_OpenIGTLink|Tracking Neuroendoscope using EM Tracker and OpenIGTLink]] (Laurent Chauvin, Junichi Tokuda, Noby Hata)
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#[[2010_Summer_Project_Week_Implementing_OpenCV_to_Slicer3_for_Neuroendoscopic_Surgery|Implementing OpenCV to Slicer3 for Neuroendoscopic Surgery]] (Atsushi Yamada, Junichi Tokuda, Noby Hata)
  
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This event is part of the translational research efforts of [http://www.na-mic.org NA-MIC], [http://www.ncigt.org NCIGT], [http://nac.spl.harvard.edu/ NAC], [http://catalyst.harvard.edu/home.html Harvard Catalyst], and [http://www.cimit.org CIMIT].  It is an expansion of the NA-MIC Summer Project Week that has been held annually since 2005. It will be held every summer at MIT and Brigham and Womens Hospital in Boston, typically during the last full week of June, and in Salt Lake City in the winter, typically during the second week of January. 
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=== Radiotherapy ===
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#[[2010_Summer_Project_Week_DICOM_RT|Dicom RT Plugin]] (Greg Sharp, Tamas Ungi)
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#[[2010_Summer_Project_Week_HandN_Cancer|Adaptive Radiation Therapy for H&N Cancer]] (Marta Peroni,Polina Golland,Greg Sharp)
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#[[2010_Summer_Project_Week_Seg_Adapt_HNT|Segmentation for Adaptive Radiotherapy for Head, Neck, and Thorax]] (Ivan Kolesov, Greg Sharp, and Allen Tannenbaum )
  
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A summary of all past NA-MIC Project Events is available [[Project_Events#Past|here]].
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=== Analysis ===
 +
#[[2010_NAMIC_Project_week:IA-FEMesh| IA-FEMesh Slicer3 Finite Meshing Module]] (N Grosland, V Magnotta, C Lisle, S Pieper)
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#[[2010_Summer_Project_Week_Cortical_Thickness_Analysis|Cortical Thickness Analysis]] (Clement Vachet, Heather Cody Hazlett, Martin Styner)
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#[[2010_Summer_Project_Week_Mouse_Brain_Cortical_Thickness_Analysis|Mouse Brain Cortical Thickness Analysis]] (Joohwi Lee, Ipek Oguz, Martin Styner)
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#[[2010_Summer_Project_Week_Primate image analysis using the standard Slicer pipeline|Primate Image Analysis using the Standard Slicer Pipeline]] (Yundi Shi, Martin Styner, Clement Vache, Mar Sanchez, Andriy Fedorov)
 +
#[[2010_Summer_Project_Week_MRSI_module_and_SIVIC_interface| MRSI Module and SIVIC Interface]] (B Menze,  M Phothilimthana, J Crane (UCSF), B Olson (UCSF), P Golland)
 +
#[[2010_Summer_Project_Week_FractureClassification_Brainstorming|Femoral Fracture Classification Brainstorming Session]] (Karl Fritscher, Vince Magnotta, Peter Karasev, Curt Lisle, Ron Kikinis)
 +
#[[2010_Summer_Project_Week_Computer_Aided_Photodynamic_Therapy| Computer Aided Photodynamic Therapy]] (E Pietka, D Spinczyk, P Szabelak)
 +
#[[2010_Summer_Project_Week_Quantification_Of_Lesion_Diffusion_Disruption| Quantification of Lesion Diffusion Disruption]] (M Scully, H J Bockholt)
 +
#[[2010_Summer_Project_Week_Lupus_Lesion_Segmentation_and_Review_Statistics|Lupus Lesion Segmentation and Review Statistics]] (M Scully, H J Bockholt)
  
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== Logistics ==
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===[[Microscopy Image Analysis]] ===
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*'''Dates:''' June 21-25, 2010
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# [[ 2010 Project Week DICOM supplement 145 | DICOM supplement 145 ]] : Microscopy Image in the Dicom Standard (Mathieu Malaterre, Alex. Gouaillard)
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*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].
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# [[ 2010 Summer Project Week Microscopy extensions for ITK | Microscopy Extensions for ITK]]: Convolution, Deconvolution, Wavelets and More ( Gaetan Lemhann, Alex. Gouaillard )
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*'''REGISTRATION:''' Please click [http://guest.cvent.com/i.aspx?4W%2cM3%2c8e73686a-1432-40f2-bc78-f9e18d8bce00 here] to do an on-line registration for the meeting that will allow you to pay by credit card, or send a check.
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# [[Import/Export Farsight-GoFigure results|Import/Export Farsight - GoFigure Results]] (Arnaud Gelas, Lydie Souhait, Kedar Grama, Raghav Padmanabhan, Sean Megason, Badri Roysam)
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*'''Registration Fee:''' $260 (covers the cost of breakfast, lunch and coffee breaks for the week).
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# [[JPEG2000 and HDF5 Image Readers in ITK]] (Kishore Mosaliganti, Luis Ibanez, Sean Megason)
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*'''Hotel:''' We have reserved a block of rooms  at the Boston Marriott Cambridge Hotel, Two Cambridge Center, 50 Broadway, Cambridge, MA 02142. (Phone: 617.252.4405, Fax: 617.494.6565) [http://www.marriott.com/hotels/travel/BOSCB?groupCode=NAMNAMA&app=resvlink&fromDate=6/20/10&toDate=6/25/10  Please click here to reserve.] You will be directed to the property's home page with the group code already entered in the appropriate field. All you need to do is enter your arrival date to begin the reservation process.  
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# [[ITK Spherical Harmonics filter for shape analysis of cell nuclei|ITK Spherical Harmonics Filter for Shape Analysis of Cell Nuclei]] (Shantanu Singh, Kishore Mosaliganti, Arnaud Gelas, Sean Megason, Raghu Machiraju)
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# [[ITK Analysis of Large Histology Datasets]] (Liya Ding, Kun Huang, Sean Megason, Raghu Machiraju)
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  ''' All reservations must be made by Tuesday, June 1, 2010 to receive the discounted rate of'''
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# [[CTK Transfer function widget|CTK Transfer Function Widget]] (Nicolas Rannou, Julien Finet, Arnaud Gelas, Stever Pieper)
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  ''' $189/night/room (plus tax).'''
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# [[Seedings results comparison|Seedings Results Comparison]] (Antonin Perrot-Audet, Raghav Padmanabhan, Kishore Mosaliganti, Badri Roysam, Sean Megason)
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  ''' This rate is good only through June 1.'''
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# [[ITK GPAC level set|ITK Multiphase and GPAC Level Sets]] (K. Palaniappan, Ilker Ersoy, Filiz Bunyak, Kishore Mosaliganti, Sean Megason)
 +
# [[MedianTexture|Median Binary Pattern Texture Measures for Cell Nuclei Segmentation]] (Adel Hafiane, Lucas Menand, K. Palaniappan, Sean Megason)
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# [[StandardsInterfaces|Standards and Interfaces for Microscopy Image Analysis in ITK]] (whoever has an opinion, Sean Megason)
  
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Please note that if you try to reserve a room outside of the block on the shoulder nights via the link, you will be told that the group rate is not available for the duration of your stay. To reserve those rooms, which might not be at the group rate because it is based upon availability, please call Marriott Central Reservations at 1-800-228-9290.
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=== NA-MIC Kit Internals ===
 +
#[[2010 NAMIC Project week: Module Inventory|Module Inventory]] (Steve, Jim)
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#[[2010 NAMIC Project week: Viewer Manager Factory|Viewer Manager Factory]] (Alex Yarmarkovich, Kilian, Steve, Nicole)
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#[[2010 NAMIC Project week: Programmatic use of Volume Rendering module|Programmatic use of Volume Rendering Module]] (Andriy Fedorov, Yanling Liu, Alex Yarmarkovich, Jim Barabas, Johannes Schick)
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#[[2010 NAMIC Project week:Inventory of Volume Rendering Functionality|Inventory of Volume Rendering Functionality]] (Jim Barabas, Noby Hata)
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#[[2010_NAMIC_Project_week:Slicer4Icons|Consistent Visual Language for Slicer4: Icon Rework Marathon]] (Wendy Plesniak)
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#[[2010_NAMIC_Project_week:LongitudinalPETSUV_Wizard | Slicer Wizard for PET/CT Workflow]] (Wendy Plesniak, Ron Kikinis, Alexander Zaitsev)
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#[[2010_Summer_Project_Week_PythonQt|PythonQt and Console Widget]] (Steve Pieper, Jean-Christophe Fillion-Robin)
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#[[2010_Summer_Project_Week_VTKWidgets|VTKWidgets]] (Jean-Christophe Fillion-Robin, Will Schroeder, Nicole Aucoin, Wendy, Ron Kikinis)
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#[[2010_Summer_Project_Week_Superbuild |Superbuild ]](David Partyka, Steve Pieper, Katie Hayes)
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#[[Paraview Support for Computational Anatomy]] (Michel Audette, Mike Bowers)
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#[[2010 NAMIC Project week: Real-Time Volume Rendering for Virtual Colonoscopy|Real-Time Volume Rendering for Virtual Colonoscopy]] (Hiro Yoshida, Yin Wu, Steve Pieper, Ron Kikinis)
  
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*Here is some information about several other Boston area hotels that are convenient to NA-MIC events: [[Boston_Hotels|Boston_Hotels]]. Summer is tourist season in Boston, so please book your rooms early.
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=== Workflows and Integration ===
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*For hosting projects, we are planning to make use of the NITRC resources.  See [[NA-MIC_and_NITRC | Information about NITRC Collaboration]]
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# [[Summer_project_week_2010_Workflows_SOA|Workflows and Service Oriented Architecture Solutions for Slicer3 Modules]] (Alexander Zaitsev, Wendy Plesniak, Charles Guttmann, Ron Kikinis)
  
 
==Agenda==
 
==Agenda==
  
 
{|border="1"
 
{|border="1"
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|-style="background: #b0d5e6; color: #02186f"
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|-style="background: #b0d5e6; color: #02186f; font-size: 130%"  
 
!Time
 
!Time
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!width="200px"|Monday, June 21
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!width="250px"|Monday, June 21
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!width="200px"|Tuesday, June 22
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!width="250px"|Tuesday, June 22
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!width="200px"|Wednesday, June 23
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!width="250px"|Wednesday, June 23
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!width="200px"|Thursday, June 24
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!width="250px"|Thursday, June 24
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!width="200px"|Friday, June 25
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!width="250px"|Friday, June 25
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|-
 +
|
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|bgcolor="#dbdbdb"|'''Project Presentations'''
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|bgcolor="#6494ec"|'''NA-MIC Update Day'''
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|
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|bgcolor="#88aaae"|'''IGT Day'''
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|bgcolor="#faedb6"|'''Reporting Day'''
 
|-
 
|-
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|8:30
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|bgcolor="#ffffdd"|'''8:30am'''
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|rowspan="5"|
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|
 
|bgcolor="#ffffaa"|Breakfast
 
|bgcolor="#ffffaa"|Breakfast
 
|bgcolor="#ffffaa"|Breakfast
 
|bgcolor="#ffffaa"|Breakfast
Line 52: Line 136:
 
|bgcolor="#ffffaa"|Breakfast
 
|bgcolor="#ffffaa"|Breakfast
 
|-
 
|-
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|9:00-9:45
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|bgcolor="#ffffdd"|'''9am-12pm'''
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|NA-MIC Kit Update (Jim Miller) - include: Module nomenclature (Extensions: cmdline vs loadable, Built-in)<br>_____________________<br> QT - include: Superbuild demo by Dave P.
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|
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|rowspan="4"|'''Breakout Session:''' [[2010 Project Week Breakout Session: ITK|ITK]] (Luis Ibanez)
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|'''9am:''' [[Media:NAMIC Kit-2010-6-22.ppt|NA-MIC Kit Update]] (Jim Miller)
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|rowspan="4"|'''Breakout Session:''' [[2010 Summer Project Week Breakout Session:OpenIGTLink|OpenIGTLink]]
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[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
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|rowspan="4"|[[#Projects|Project Progress Updates]]
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<br>----------------------------------------<br>
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|-
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'''9:20am:''' [[Media:2010_Project_Week_Slicer.ppt|3D Slicer Update]] (Steve Pieper)
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|9:45-10:30
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<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
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|bgcolor="#c1c2ec"|3D Slicer Update (Steve Pieper)
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<br>----------------------------------------<br>
−
|-
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'''10am:''' Superbuild Demo (Dave Partyka)
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|10:30-11:00
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<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
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|OpenIGTLink Update (Junichi Tokuda)
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<br>----------------------------------------<br>
−
|-
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'''10:15am:''' Break
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|11:00-12:00
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<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
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|bgcolor="#c1c2ec"|Slicer Hands-on Workshop (Randy Gollub, Sonia Pujol)
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<br>----------------------------------------<br>
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'''10:30-11am:''' [[Media:2010_Project_Week_OpenIGTLink.ppt|OpenIGTLink Update]] (Junichi Tokuda)
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<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
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<br>----------------------------------------<br>
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'''11am-12pm:''' [[2010_Summer_Project_Week_Slicer_Hands-on_Workshop|Slicer Hands-on Workshop]] (Randy Gollub, Sonia Pujol)
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<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]
 +
|'''9am-12pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2010 Project Week Breakout Session: ITK|ITK]] (Luis Ibanez)
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<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]
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|'''9am-5pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2010 Summer Project Week Breakout Session:OpenIGTLink|OpenIGTLink]]
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<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
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|'''10am-12pm:''' [[#Projects|Project Progress Updates]]
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<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
 
|-
 
|-
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|12:00-13:00
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|bgcolor="#ffffdd"|'''12pm-1pm'''
 
|bgcolor="#ffffaa"|Lunch
 
|bgcolor="#ffffaa"|Lunch
 
|bgcolor="#ffffaa"|Lunch
 
|bgcolor="#ffffaa"|Lunch
 
|bgcolor="#ffffaa"|Lunch
 
|bgcolor="#ffffaa"|Lunch
 
|bgcolor="#ffffaa"|Lunch
 
|bgcolor="#ffffaa"|Lunch
−
|bgcolor="#ffffaa"|Lunch boxes
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|bgcolor="#ffffaa"|Lunch boxes; Adjourn by 1:30pm
 
|-
 
|-
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|12:45-13:00
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|bgcolor="#ffffdd"|'''1pm-5:30pm'''
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|
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|'''1-1:05pm: <font color="#503020">Ron Kikinis: Welcome</font>'''
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|
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[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
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|bgcolor="#ccffcc"|[[Events:TutorialContestJune2010|Tutorial Contest Winner Announcement]]
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<br>----------------------------------------<br>
 +
'''1:05-3:30pm:''' [[#Projects|Project Introductions]] (all Project Leads)
 +
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
 +
<br>----------------------------------------<br>
 +
'''3:30-5:30pm: Tutorial:''' [[2010 Summer Project Week Breakout: Getting Started with Qt|Getting Started with Qt]] (Adam Weinrich, Nokia)
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<br>[[MIT_Project_Week_Rooms#32-155|32-155 (Stata Lecture Hall)]]
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|'''1-3pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2010_Summer_Project_Qt_tutorial|QT/Slicer]] (Steve, JC, J2)
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<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]
 +
<br>----------------------------------------<br>
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'''3-4pm:''' [[Summer_2010_Tutorial_Contest|Tutorial Contest Presentations]]
 +
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
 +
<br>----------------------------------------<br>
 +
'''4-5pm: <font color="#4020ff">Breakout Session:'''</font>
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<br> [[2010 Summer Project Week Breakout Session: Data Management |Data Management]] (Stephen Aylward)
 +
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]
 +
|'''12:45-1pm:''' [[Events:TutorialContestJune2010|Tutorial Contest Winner Announcement]]
 +
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
 +
<br>----------------------------------------<br>
 +
'''1-3pm: <font color="#4020ff">Breakout Session:'''</font><br> [[Microscopy_Image_Analysis|Microscopy Image Analysis]] (Sean Megason)
 +
<br>[[MIT_Project_Week_Rooms#Kiva|Kiva Room]]
 +
<br>----------------------------------------<br>
 +
'''3-5pm: <font color="#4020ff">Breakout Session:'''</font><br>
 +
[[2010 Summer Project Week Breakout Session:QA Training|QA Training]] (Luis Ibanez)
 +
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]
 +
<br>----------------------------------------<br>
 +
'''3-4pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2010 Summer Project Week Breakout Session:VTK Widget|VTK Widgets]] (Nicole, Kilian, JC)
 +
<br>[[MIT_Project_Week_Rooms#32-261|32-261 Room]]
 +
<br>----------------------------------------<br>
 +
<br>'''5pm: <font color="#4020ff">Reception'''</font><br>
 +
<br>[[MIT_Project_Week_Rooms#R&D Pub|R&D Pub]]
 +
|'''1-2pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2010 Summer Project Week Breakout Session:GWE|GWE]] (Marco Ruiz)
 +
<br>----------------------------------------<br>
 +
'''2-3pm:''' Simple Git (Steve Pieper) [[media:Simple Git-pieper-2010-06-24.ppt|(Slides)]]
 +
<br>----------------------------------------<br>
 +
'''3-4pm: <font color="#4020ff">Breakout Session:'''</font><br>
 +
[[2010 Summer Project Week Breakout Session: Volume Rendering|Volume Rendering Demos and Discussion]] (Yin Wu, Steve Pieper)
 
|
 
|
 +
|-
 +
|bgcolor="#ffffdd"|'''5:30pm'''
 +
|bgcolor="#f0e68b"|Adjourn for the day
 +
|bgcolor="#f0e68b"|Adjourn for the day
 +
|bgcolor="#f0e68b"|Adjourn for the day
 +
|bgcolor="#f0e68b"|Adjourn for the day
 
|
 
|
−
|-
 
−
|13:00-13:30
 
−
|rowspan="5"|<font color="#0000cc">Ron Kikinis: Welcome<br> </font> (5 minutes)<br>_____________________<br> Introduce [[#Projects|Projects]] using templated wiki pages (all Project Leads) ([http://wiki.na-mic.org/Wiki/index.php/Project_Week/Template Wiki Template])
 
−
|rowspan="4"|'''Breakout Session:''' QT/Slicer (Steve, JC, J2) (w/ possible QnA with QT experts)
 
−
|rowspan="4"|'''Breakout Session:''' [[Microscopy_Image_Analysis|Microscopy Image Analysis]] (Sean Megason)
 
−
|rowspan="2"|'''Breakout Session:''' [[2010 Summer Project Week Breakout Session:GWE|GWE]] (Marco Ruiz)
 
−
|bgcolor="#FFD600"|Adjourn by 1:30pm
 
−
|-
 
−
|13:30-14:00
 
−
|rowspan="9"|
 
−
|-
 
−
|14:00-14:30
 
−
|bgcolor="#ccffcc"|Build Instructions: [http://www.commontk.org/index.php/Build_Instructions#Simple_Git  Simple Git] (Steve Pieper)
 
−
|-
 
−
|14:30-15:00
 
−
|rowspan="6"|
 
−
|-
 
−
|15:00-15:30
 
−
|rowspan="2" style="background: #ccffcc;"|[[Summer_2010_Tutorial_Contest|Tutorial Contest Presentations]]
 
−
|rowspan="5"|'''Breakout Session:''' [[2010 Summer Project Week Breakout Session:QA Training|QA Training]] (Luis Ibanez)<br>_____________________<br>'''Breakout Session:''' [[2010 Summer Project Week Breakout Session:VTK Widget|VTK Widget]] (Nicole, Kilian, JC)
 
−
|-
 
−
|15:30-16:00
 
−
|rowspan="4" style="background: #ccffcc;"|Tutorial: [[2010 Summer Project Week Breakout: Getting Started with Qt|Getting Started with Qt]] (Adam Weinrich, Nokia)
 
−
|-
 
−
|16:00-16:30
 
−
|rowspan="3"|'''Breakout Session:''' [[2010 Summer Project Week Breakout Session: Data Management|Data Management]] (Dan Marcus, Stephen Aylward)
 
−
|-
 
−
|16:30-17:00
 
−
|-
 
−
|17:00-17:30
 
−
|-
 
−
|17:30
 
−
|bgcolor="#FFD600"|Adjourn for the day
 
−
|bgcolor="#FFD600"|Adjourn for the day
 
−
|bgcolor="#FFD600"|Adjourn for the day
 
−
|bgcolor="#FFD600"|Adjourn for the day
 
 
|}
 
|}
−
=== Monday, June 21, 2010 ===
 
−
** noon-1pm lunch
 
−
**1pm: Welcome (Ron Kikinis)
 
−
** 1:05-3:30pm Introduce [[#Projects|Projects]] using templated wiki pages (all Project Leads) ([http://wiki.na-mic.org/Wiki/index.php/Project_Week/Template Wiki Template])
 
−
** 3:30-5:30pm Tutorial: [[2010 Summer Project Week Breakout: Getting Started with Qt]] (Adam Weinrich, Nokia)
 
  
−
=== Tuesday, June 22, 2010 ===
+
Please note:
−
** 8:30am breakfast
+
*We need to empty room by 1:30pm on Friday.  You are welcome to use wireless in Stata.
−
**9-9:45am: NA-MIC Kit Update (Jim Miller) - include Module nomenclature (Extensions: cmdline vs loadable, Built-in), QT, Include Superbuild demo by Dave P.
+
*Please sign up for the Slicer Developer [http://www.slicer.org/pages/Mailinglist mailing lists]
−
**9:45-10:30am 3D Slicer Update (Steve Pieper)
+
*Next Project Week [[AHM_2011| January 3-7, 2011, Salt Lake City, Utah]]
−
**10:30-11am OpenIGTLink Update (Junichi Tokuda)
 
−
**11-12pm: Slicer Hands-on Workshop (Randy Gollub, Sonia Pujol)
 
−
** noon lunch
 
−
** 1-3pm: Breakout Session: QT/Slicer (Steve, JC, J2) (w/ possible QnA with QT experts)
 
−
** 3pm: [[Summer_2010_Tutorial_Contest|Tutorial Contest Presentations]]
 
−
** 4-5pm [[2010 Summer Project Week Breakout Session: Data Management]] (Dan Marcus, Stephen Aylward)
 
−
** 5:30pm adjourn for day
 
  
−
=== Wednesday, June 23, 2010 ===
+
==Background==
−
** 8:30am breakfast
 
−
** 9am-12pm Breakout Session: [[2010 Project Week Breakout Session: ITK]] (Luis Ibanez)
 
−
** noon lunch
 
−
**12:45pm: [[Events:TutorialContestJune2010|Tutorial Contest Winner Announcement]]
 
−
**1-3pm: Breakout Session: [[Microscopy_Image_Analysis]] (Sean Megason)
 
−
**3-5pm: Breakout Session: [[2010 Summer Project Week Breakout Session:QA Training]] (Luis Ibanez)
 
−
**3-5pm: Breakout Session: [[2010 Summer Project Week Breakout Session:VTK Widget]] (Nicole, Kilian, JC)
 
−
** 5:30pm adjourn for day
 
  
−
=== Thursday, June 24, 2010 ===
+
We are pleased to announce the 11th PROJECT WEEK of hands-on research and development activity for applications in Image-Guided Therapy, Neuroscience, and several additional areas of biomedical research that enable personalized medicine. Participants will engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, medical imaging sequence development, tracking experiments, and clinical application. The main goal of this event is to move forward the translational research deliverables of the sponsoring centers and their collaborators. Active and potential collaborators are encouraged and welcome to attend this event. This event will be set up to maximize informal interaction between participants. 
−
** 8:30am breakfast
 
  
−
** 9am-5pm: Breakout Session: [[2010 Summer Project Week Breakout Session:OpenIGTLink|OpenIGTLink]]
+
Active preparation begins on Thursday, April 15th at 3pm ET, with a kick-off teleconference.  Invitations to this call will be sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties who have expressed an interest in working with these centers. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient coverage for all. Subsequent teleconferences will allow for more focused discussions on individual projects and allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading up to the meeting, all project teams will be asked to fill in a template page on this wiki that describes the objectives and plan of their projects.
−
** noon lunch
 
−
** 1-2pm: [[2010 Summer Project Week Breakout Session:GWE]] (Marco Ruiz)
 
−
** 2-2:30pm: [http://www.commontk.org/index.php/Build_Instructions#Simple_Git Simple Git] (Steve Pieper)
 
−
** 5:30pm adjourn for day
 
  
−
=== Friday, June 25, 2010 ===
+
The event itself will start off with a short presentation by each project team, driven using their previously created description, and will help all participants get acquainted with others who are doing similar work. In the rest of the week, about half the time will be spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half will be spent in project teams, doing hands-on project work.  The hands-on activities will be done in 30-50 small teams of size 2-4, each with a mix of multi-disciplinary expertise. To facilitate this work, a large room at MIT will be setup with several tables, with internet and power access, and each computer software development based team will gather on a table with their individual laptops, connect to the internet to download their software and data, and be able to work on their projects.  Teams working on projects that require the use of medical devices will proceed to Brigham and Women's Hospital and carry out their experiments there. On the last day of the event, a closing presentation session will be held in which each project team will present a summary of what they accomplished during the week.
−
** 8:30am breakfast
 
−
** 10am-noon: [[#Projects|Project Progress Updates]]
 
−
*** Noon: Lunch boxes and adjourn by 1:30pm.
 
−
***We need to empty room by 1:30.  You are welcome to use wireless in Stata.
 
−
***Please sign up for the developer [http://www.slicer.org/pages/Mailinglist mailing lists]
 
−
***Next Project Week [[AHM_2011|in Utah]]
 
  
−
==Projects==
+
This event is part of the translational research efforts of [http://www.na-mic.org NA-MIC], [http://www.ncigt.org NCIGT], [http://nac.spl.harvard.edu/ NAC], [http://catalyst.harvard.edu/home.html Harvard Catalyst], and [http://www.cimit.org CIMIT].  It is an expansion of the NA-MIC Summer Project Week that has been held annually since 2005. It will be held every summer at MIT and Brigham and Women's Hospital in Boston, typically during the last full week of June, and in Salt Lake City in the winter, typically during the second week of January. 
  
 +
== Logistics ==
 +
*'''Dates:''' June 21-25, 2010
 +
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].
 +
*'''REGISTRATION:''' Please click [http://guest.cvent.com/i.aspx?4W%2cM3%2c8e73686a-1432-40f2-bc78-f9e18d8bce00 here] to do an on-line registration for the meeting that will allow you to pay by credit card, or send a check.
 +
*'''Registration Fee:''' $260 (covers the cost of breakfast, lunch and coffee breaks for the week).
 +
*'''Hotel:''' We have reserved a block of rooms  at the Boston Marriott Cambridge Hotel, Two Cambridge Center, 50 Broadway, Cambridge, MA 02142. (Phone: 617.252.4405, Fax: 617.494.6565)  [http://www.marriott.com/hotels/travel/BOSCB?groupCode=NAMNAMA&app=resvlink&fromDate=6/20/10&toDate=6/25/10  Please click here to reserve.] You will be directed to the property's home page with the group code already entered in the appropriate field. All you need to do is enter your arrival date to begin the reservation process.
 +
 
 +
*''' All reservations must be made by Tuesday, June 1, 2010 to receive the discounted rate of'''
 +
*''' $189/night/room (plus tax).'''
 +
*''' This rate is good only through June 1, 2010.'''
  
 +
Please note that if you try to reserve a room outside of the block on the shoulder nights via the link, you will be told that the group rate is not available for the duration of your stay. To reserve those rooms, which might not be at the group rate because it is based upon availability, please call Marriott Central Reservations at 1-800-228-9290.
  
−
=== Segmentation ===
+
*Here is some information about several other Boston area hotels that are convenient to NA-MIC events: [[Boston_Hotels|Boston_Hotels]]. Summer is tourist season in Boston, so please book your rooms early.
−
#[[2010_Summer_Project_Week_Robust_Statistics_Segmenter_Slicer_Module|Robust Statistics Segmenter Slicer Module]] (Yi Gao, Allen Tannenbaum, Ron Kikinis)
+
*For hosting projects, we are planning to make use of the NITRC resources. See [[NA-MIC_and_NITRC | Information about NITRC Collaboration]]
−
#[[2010_Summer_Project_Week_Multi_scale_Shape_Based_Segmentation_for_the_Hippocampus|Multi-scale Shape Based Segmentation for the Hippocampus]] (Yi Gao, Allen Tannenbaum)
 
−
#[[2010_Summer_Project_Week_SegmentationMeshEmbeddedContours|Segmentation on Mesh Surfaces Using Geometric Information]] (Peter Karasev, Karol Chudy, Allen Tannenbaum, GT; Ron Kikinis, BWH)
 
−
#[[2010_Summer_Project_Week/The Vascular Modeling Toolkit in 3D Slicer|The Vascular Modeling Toolkit in 3D Slicer]] (Daniel Haehn, Luca Antiga, Kilian Pohl, Steve Pieper, Ron Kikinis)
 
−
#[[2010_Summer_Project_Week_Prostate_MRI_Segmentation|Prostate Segmentation from MRI]] (Andriy Fedorov, Yi Gao)
 
−
#[[2010_Summer_Project_Week_SPECTRE|SPECTRE: Skull Stripping integration with Slicer]] (Nicole Aucoin, Min Chen)
 
−
#[[2010_Summer_Project_Week_White Matter Lesion segmentation|White Matter Lesion segmentation]] (Minjeong Kim, Xiaodong Tao, Jim Miller, Dinggang Shen)
 
−
#[[2010_Summer_Project_Week_Left ventricular scar segmentation| LV scar segmentation display and fusion]] (Dana C. Peters, Felix Liu, BIDMC, Boston)
 
−
#[[2010_Summer_Project_Week_EMSegmentation_kmeans|EMSegmentation: Automatic Intensity Initialization using KMeans ]](Priya Srinivasan, Daniel Haehn, Kilian Pohl, Sylvain Bouix)
 
  
−
=== Registration ===
 
−
#[[2010_Summer_Project_Week_RegistrationCaseLibrary|The 3DSlicer Registration Case Library]] (Dominik Meier)
 
−
#[[2010_Summer_Project_Week_Fiducial_Deformable_Registration|Fiducial-based deformable image registration]] (Nadya Shusharina, Greg Sharp)
 
−
#[[2010_Summer_Project_Week_HAMMER: Deformable Registration|HAMMER: Deformable Registration]] (Guorong Wu, Xiaodong Tao, Jim Miller, Dinggang Shen)
 
−
#[[2010_Summer_Project_Week_Best_Regularization_Term_for_Demons_Registration_Algorithm|Best Regularization Term for Demons Registration Algorithm]] (Rui Li, Greg Sharp)
 
−
#[[2010_Summer_Project_Week_RegistrationEvaluation|Evaluation of Registration in Slicer]] (James Fishbaugh, Guido Gerig, Domink Meier)
 
−
#[[2010_Summer_Project_Week_MR_to_Ultrasound_Registration_Methodology|MR to Ultrasound Registration Methodology]] (Dieter Hahn, William Wells, Joachim Hornegger, Tina Kapur, Stephen Aylward)
 
−
#[[2010_Summer_Project_Week_Groupwise_Registration|Groupwise Registration]] (Ryan Eckbo, Jim Miller, Hans Johnson, Kilian Pohl, Daniel Haehn)
 
−
 
−
=== IGT ===
 
−
#[[2010_Summer_Project_Week_MR_to_CT_Registration_for_Prostate_Brachytherapy_Dose_Calculation|MR to CT Registration for Prostate Brachytherapy Dose Calculation]] (Andriy Fedorov, Dominik Meier, Hans Johnson)
 
−
#Intraoperative Brain Shift Monitoring Using Shear Mode Transcranial Ultrasound (Jason White, Steve Pieper?, Pratik Patel?)
 
−
#Prostate Intervention(Junichi,  Sam Song, Tamas Ungi)
 
−
# Liver Ablation (Haiying Liu)
 
−
# [[2010_Summer_Project_Week_BrainLab_Aurora_Hybrid_Navigation|BrainLab-Aurora Hybrid Navigation]] (Isaiah Norton, Dan Marcus, Noby Hata)
 
−
#[[2010_Summer_Project_Week_Dynamic_Image_Fusion_for_Guidance_of_Cardiac_Therapies|Dynamic Image Fusion for Guidance of Cardiac Therapies]] (Feng Li)
 
−
# [[2010_Summer_Project_Week_PerkStationModule|PerkStation Module]] (Tamas Ungi, Xiaodong Tao)
 
−
#[[2010_Summer_Project_Week_Co-registration_of_PET_and_DWI_Images_for_the_targeting_of_Glioma_Biopsies|Co-registration of PET and DWI Images for the targeting of Glioma Biopsies]] (Gareth Smith, Dominik Meir, Vince Magnotta)
 
−
#[[2010_Summer_Project_Week_Implementing_Open_IGT_Link_to_Virtual_Place_for_research_support|Implementing Open IGT Link to Virtual Place for research support]] (Nicholas Herlambang, Noby Hata)
 
−
 
−
=== Radiotherapy ===
 
−
#[[2010_Summer_Project_Week_DICOM_RT|Dicom RT plugin]] (Greg Sharp, Tamas Ungi)
 
−
#[[2010_Summer_Project_Week_HandN_Cancer|Adaptive Radiation Therapy for H&N cancer]] (Marta Peroni,Polina Golland,Greg Sharp)
 
−
#[[2010_Summer_Project_Week_Seg_Adapt_HNT|Segmentation for Adaptive Radiotherapy for Head, Neck, and Thorax]] (Ivan Kolesov, Greg Sharp, and Allen Tannenbaum )
 
−
 
−
=== Analysis ===
 
−
#Femoral Fracture Classification Brainstorming Session (Karl F, Vince M, Peter Karasev, Curt Lisle, Ron)
 
−
#[[2010_Summer_Project_Week_Cortical_Thickness_Analysis|Cortical thickness analysis]] (Clement Vachet, Heather Cody Hazlett, Martin Styner)
 
−
#[[2010_Summer_Project_Week_MRSI_module_and_SIVIC_interface| MRSI module and SIVIC interface]] (B Menze,  M Phothilimthana, J Crane (UCSF), B Olson (UCSF), P Golland)
 
−
#[[2010_Summer_Project_Week_Computer_Aided_Photodynamic_Therapy| Computer_Aided_Photodynamic_Therapy]] (E Pietka, D Spinczyk, P Szabelak)
 
−
#[[2010_NAMIC_Project_week:IA-FEMesh| IA-FEMesh Slicer3 Finite Meshing Module]] (N Grosland, V Magnotta, C Lisle, S Pieper)
 
−
 
−
===[[Microscopy Image Analysis]] ===
 
−
# [[ 2010 Project Week DICOM supplement 145 | DICOM supplement 145 ]] : Microscopy Image in the Dicom Standard (Mathieu Malaterre, Alex. Gouaillard)
 
−
# [[ 2010 Summer Project Week Microscopy extensions for ITK | Microscopy Extensions for ITK ]]: convolution, deconvolution, wavelets and more ( Gaetan Lemhann, Alex. Gouaillard )
 
−
# [[ 2010 Summer Project Week Flow Cytometry | Flow Cytometry ]] (Bertrand Moreau, Rossella Melchiotti, Alex. Gouaillard)
 
−
# [[Import/Export Farsight-GoFigure results]] (Lydie Souhait, Arnaud Gelas, Sean Megason, Badri Roysam)
 
−
# [[Farsight nuclear segmentation as GoFigure plugin]] (Arnaud Gelas, Sean Megason, Badri Roysam)
 
−
# [[ITK Spherical Harmonics filter for shape analysis of cell nuclei]] (Shantanu Singh, Arnaud Gelas, Sean Megason, Raghu Machiraju)
 
−
# [[ITK Analysis of Large Histology Datasets]] (Liya Ding, Kun Huang, Sean Megason, Raghu Machiraju)
 
−
# [[CTK Transfer function widget]] (Nicolas Rannou, Julien Finet, Stever Pieper)
 
−
# [[Seedings results comparison]] (Antonin Perrot-Audet, Kishore Mosaliganti, Badri Roysam, Sean Megason)
 
−
# [[ITK GPAC level set|ITK Multiphase and GPAC level sets]] (K. Palaniappan, Ilker Ersoy, Filiz Bunyak, Kishore Mosaliganti, Sean Megason)
 
−
# [[JPEG2000 and HDF5 Image Readers in ITK]] (Kishore Mosaliganti, Luis Ibanez, Sean Megason)
 
−
# [[MedianTexture|Median binary pattern texture measures for cell nuclei segmentation]] (Adel Hafiane, Lucas Menand, K. Palaniappan, Sean Megason)
 
−
# [[StandardsInterfaces|Standards and Interfaces for Microscopy Image Analysis in ITK]] (whoever has an opinion, Sean Megason)
 
−
 
−
=== Shape Analysis ===
 
−
#[[2010_Summer_Project_Week_Shape|Median Shape by Boundary-based Distance ]](Tammy Riklin Raviv, Sylvain Bouix)
 
−
# [[Shape Analysis projects, integration with Slicer3]] (Beatriz Paniagua, Martin Styner)
 
−
# [[Particle Based Shape Regression]] (Manasi Datar, Joshua Cates, P. Thomas Fletcher, Sylvain Gouttard, Guido Gerig, Ross Whitaker)
 
−
#[[Automatic SPHARM Shape Analysis in 3D Slicer ]] (Corentin Hamel, Clement Vachet, Beatriz Paniagua, Nicolas Augier, Martin Styner)
 
−
#[[2010_Summer_Project_Week_Shape_Test_Bench|Shape Test Bench]] (Marc Niethammer, Sylvain Bouix)
 
−
 
−
=== Diffusion ===
 
−
#[[2010_Summer_Project_Week_Diffusion|Fluid Mechanics Based Tractography ]](Nathan Hageman)
 
−
#[[Efficient Diffusion Connectivity via Multi­directional F­star]] (Alexis Boucharin, Clement Vachet, Yundi Shi, Mar Sanchez, Martin Styner)
 
−
#[[2010_Summer_Project_Two_Tensor|Implementing Two-tensor tractography in Slicer (Python) ]](Stefan Leinhard, James Malcolm, Demian Wasserman, Yogesh Rathi)
 
−
#[[Application of the DTI pipeline to the teenage substance abuse study]] (Gopalkrishna Veni, Sarang Joshi, Ross Whitaker)
 
−
#[[NAMIC Tools Suite for DTI analysis]] (Hans Johnson, Joy Matsui, Vincent Magnotta, Sylvain Gouttard)
 
−
#[[2010_Summer_Project_QSpace_Reconstruction_for_Diffusion_Spectrum_Imaging_Data|QSpace Imaging Reconstruction for Diffusion Spectrum Imaging Data]] (Sudhir Pathak)
 
−
 
−
=== NA-MIC Kit Internals ===
 
−
#[[2010 NAMIC Project week: Module Inventory|Module Inventory]] (Steve, Jim)
 
−
#[[2010 NAMIC Project week: Viewer Manager Factory|Viewer Manager Factory]] (Alex Yarmarkovich, Kilian, Steve, Nicole)
 
−
#[[2010 NAMIC Project week: Programmatic use of Volume Rendering module|Programmatic use of Volume Rendering module]] (Andrey Fedorov, Yanling Liu, Alex Yarmarkovich)
 
−
#[[2010_NAMIC_Project_week:Slicer4Icons|Consistent visual language for Slicer4: icon rework marathon]] (Wendy Plesniak)
 
−
#[[2010_NAMIC_Project_week:LongitudinalPETSUV_Wizard | Slicer Wizard for PET/CT workflow]] (Wendy Plesniak, Ron Kikinis)
 
−
#[[2010_Summer_Project_Week_PythonQt|PythonQt and console widget]] (Steve Pieper, Jean-Christophe Fillion-Robin)
 
−
#[[2010_Summer_Project_Week_VTKWidgets|VTKWidgets]] (Jean-Christophe Fillion-Robin, Will Schroeder, Nicole Aucoin, Wendy, Ron Kikinis)
 
−
#[[2010_Summer_Project_Week_Superbuild |Superbuild ]]Superbuild (David Partyka, Steve Pieper, Katie Hayes)
 
−
#[[Paraview Support for Computational Anatomy]] (Michel Audette, Mike Bowers)
 
  
 
== Preparation ==
 
== Preparation ==
Line 268: Line 268:
 
<big>'''NOTE:'''</big> <font color="maroon">THIS IS AN AUTOMATICALLY GENERATED LIST FROM THE REGISTRATION WEBSITE. ATTENDEES SHOULD '''NOT''' EDIT THIS, BUT [http://guest.cvent.com/i.aspx?4W%2cM3%2c8e73686a-1432-40f2-bc78-f9e18d8bce00 REGISTER BY CLICKING HERE.]</font>  
 
<big>'''NOTE:'''</big> <font color="maroon">THIS IS AN AUTOMATICALLY GENERATED LIST FROM THE REGISTRATION WEBSITE. ATTENDEES SHOULD '''NOT''' EDIT THIS, BUT [http://guest.cvent.com/i.aspx?4W%2cM3%2c8e73686a-1432-40f2-bc78-f9e18d8bce00 REGISTER BY CLICKING HERE.]</font>  
  
−
# Anderson Peter , GE Navigation (Retired)
+
#Yousef Al-Kofahi, CompuCyte Corporation
−
# Aucoin Nicole , BWH
+
#Peter Anderson, retired
−
# Audette Michel , Kitware
+
#Nicole Aucoin, Brigham and Women's Hospitall
−
# Aylward Stephen , Kitware, Inc
+
#Michel Audette, Kitware, Inc.
−
# Boucharin Alexis , UNC Neuro Image Research and Analysis Laboratories
+
#Stephen Aylward, Kitware, Inc.
−
# Bouix Sylvain , BWH
+
#Jim Barabas, MIT
−
# Bowers Michael , Johns Hopkins University
+
#Barrett Ryan, Brigham and Women's Hospital
−
# Budin Francois , UNC
+
#Alexis Boucharin, UNC Neuro Image Research and Analysis Laboratories
−
# Burdette Everette , Acoustic MedSystems, Inc.
+
#Sylvain Bouix, Brigham and Women's Hospital
−
# CHAUVIN Laurent , Brigham and Women's Hospital
+
#Michael Bowers, Johns Hopkins University
−
# Chen Min , Johns Hopkins University
+
#Francois Budin, UNC
−
# Crane Jason , UCSF
+
#Everette Burdette, Acoustic MedSystems, Inc.
−
# Datar Manasi , SCI Institute
+
#Laurent Chauvin, Brigham and Women's Hospital
−
# Ding Liya , The Ohio State University
+
#Min Chen, Johns Hopkins University
−
# Eckbo Ryan , BWH
+
#Jason Crane, UCSF
−
# Ersoy Ilker , University of Missouri Columbia
+
#Nikos Chrisochoides, College of William and Mary
−
# Fedorov Andriy , Surgical Planning Lab
+
#Manasi Datar, SCI Institute
−
# Fillion-Robin Jean-Christophe , Kitware Inc.
+
#Liya Ding, The Ohio State University
−
# Finet Julien , Kitware Inc
+
#Ryan Eckbo, Brigham and Women's Hospital
−
# Fishbaugh James , SCI Institute
+
#Ilker Ersoy, University of Missouri Columbia
−
# Fritscher Karl , UMIT
+
#Andriy Fedorov, Surgical Planning Lab
−
# Gao Yi , Gerogia Tech
+
#Jean-Christophe Fillion-Robin, Kitware, Inc.
−
# GELAS Arnaud , Harvard Medical School
+
#Julien Finet, Kitware, Inc.
−
# Gorgolewski Chris , SPL
+
#James Fishbaugh, SCI Institute
−
# gouaillard alexandre , CoSMo Software
+
#Karl Fritscher, UMIT
−
# Gouttard Sylvain , SCI Institute
+
#Yi Gao, Gerogia Tech
−
# Grama Kedar , Rensselaer Polytechnic Institute
+
#Arnaud GELAS, Harvard Medical School
−
# Haehn Daniel , University of Pennsylvania
+
#Randy Gollub, MGH
−
# Hafiane Adel , ENSI-Bourges
+
#Chris Gorgolewski, Surgical Planning Laboratory
−
# Hageman Nathan , UCLA
+
#alexandre gouaillard, CoSMo Software
−
# Hahn Dieter , University Erlangen
+
#Sylvain Gouttard, SCI Institute
−
# Halle Michael , BWH/SPL
+
#Kedar Grama, Rensselaer Polytechnic Institute
−
# Hamel Corentin , UNC Chapel Hill
+
#Daniel Haehn, University of Pennsylvania
−
# Hata Nobuhiko , Brigham and Women's Hospital
+
#Adel Hafiane, ENSI-Bourges
−
# Hayes Kathryn , Brigham and Women's Hospital
+
#Nathan Hageman,
−
# Herlambang Nicholas , AZE, Ltd.
+
#Dieter Hahn, University of Erlangen
−
# Holton Leslie , Medtronic Navigation
+
#Michael Halle, Surgical Planning Laboratory, Brigham and Women's Hospital
−
# Ibanez Luis , KITWARE Inc.
+
#Corentin Hamel, UNC Chapel Hill
−
# Jagadeesan Jayender , SPL
+
#Nobuhiko Hata, Brigham and Women's Hospital
−
# Johnson Hans , University of Iowa
+
#Kathryn Hayes, Brigham and Women's Hospital
−
# Kapur Tina , Brigham and Women's Hospital
+
#Nicholas Herlambang, AZE, Ltd.
−
# Kikinis Ron , Brigham and Women's Hospital
+
#Masakatsu Hoashi,  AZE Ltd.
−
# Kim Minjeong , UNC-Chapel Hill
+
#Leslie Holton, Medtronic Navigation
−
# Kolesov Ivan , Georgia Institute of Technology
+
#Luis Ibanez, Kitware, Inc.
−
# Larson Garrett , UNC-CH
+
#Jayender Jagadeesan, Surgical Planning Laboratory, Brigham and Women's Hospital
−
# Lee Joohwi , UNC Chapel Hill
+
#Hans Johnson, University of Iowa
−
# Li Rui , MGH
+
#Tina Kapur, Brigham and Women's Hospital
−
# Lienhard Stefan , LMI
+
#Peter Karasev, Georgia Tech
−
# Lisle Curtis , KnowledgeVis, LLC
+
#Ron Kikinis, Brigham and Women's Hospital
−
# Liu Felix , Beth Israel Deaconess Medical Center
+
#Minjeong Kim, UNC-Chapel Hill
−
# Liu Yanling , SAIC-Frederick, Inc.
+
#Ivan Kolesov, Georgia Institute of Technology
−
# Liu Haiying , Brigham and Women's Hospital
+
#Garrett Larson, UNC-CH
−
# Lowekamp Bradley , Lockheed Martin
+
#Joohwi Lee, UNC Chapel Hill
−
# machiraju raghu , The Ohio State University
+
#Rui Li, MGH
−
# Magnotta Vincent , The University of Iowa
+
#Stefan Lienhard, LMI
−
# malaterre mathieu , CoSMo Software
+
#Curtis Lisle, KnowledgeVis, LLC
−
# Marcus Daniel , Washington University
+
#Haiying Liu, Brigham and Women's Hospital
−
# Marks William , Focused Ultrasound Lab, BWH, HMS
+
#Felix Liu, Beth Israel Deaconess Medical Center
−
# Mastrogiacomo Katie , Brigham and Women's Hospital
+
#Yanling Liu, SAIC-Frederick, Inc.
−
# Matsui Joy , University of Iowa
+
#Bradley Lowekamp, Lockheed Martin
−
# Megason Sean , Harvard Medical School
+
#Raghu Machiraju, The Ohio State University
−
# Meier Dominik , BWH, Boston MA
+
#Vincent Magnotta, The University of Iowa
−
# menze bjoern , CSAIL MIT
+
#Mathieu Malaterre, CoSMo Software
−
# menze bjoern , CSAIL MIT
+
#Charles Maneval, Brigham and Women's Hospital
−
# Milchenko Mikhail , WUSTL
+
#Daniel Marcus, Washington University
−
# Miller James , GE Research
+
#William Marks, Focused Ultrasound Lab, Brigham and Women's Hospital
−
# Mosaliganti Kishore , Harvard Medical School
+
#Katie Mastrogiacomo, Brigham and Women's Hospital
−
# Niethammer Marc , UNC Chapel Hill
+
#Joy Matsui, University of Iowa  
−
# Norton Isaiah , BWH Neurosurgery
+
#Sean Megason, Harvard Medical School
−
# Olson Beck , UCSF
+
#Dominik Meier, Brigham and Women's Hospital
−
# Onofrey John , Yale University
+
#Bjoern Menze, CSAIL MIT
−
# Padmanabhan Raghav , RPI
+
#Mikhail Milchenko, WUSTL
−
# Palaniappan Kannappan , university of Missouri
+
#James Miller, GE Research
−
# Paniagua Beatriz , University of North Caolina at Chapel Hill
+
#Kishore Mosaliganti, Harvard Medical School
−
# Papademetris Xenophon , Yale University
+
#Marc Niethammer, UNC Chapel Hill
−
# Partyka David , Kitware Inc
+
#Isaiah Norton, Brigham and Women's Hospital
−
# Patel Pratik , Brainlab Inc
+
#Beck Olson, UCSF
−
# Pathak Sudhir , Univeristy Of Pittsburgh
+
#John Onofrey, Yale University
−
# PECOT Thierry , Ohio State University
+
#Raghav Padmanabhan, RPI
−
# Peroni Marta , Politecnico di Milano, MIT, MGH
+
#Kannappan Palaniappan, University of Missouri
−
# Perrot-Audet Antonin , Harvard Medical School
+
#Beatriz Paniagua, University of North Carolina at Chapel Hill
−
# Pieper Steve , Isomics, Inc.
+
#Xenophon Papademetris, Yale University
−
# Plesniak Wendy , BWH
+
#Eun-Joo Park, Brigham and Women's Hospital
−
# Pohl Kilian , IBM
+
#David Partyka, Kitware, Inc.
−
# Pujol Sonia , Brigham and Women's Hospital
+
#Pratik Patel,
−
# Rannou Nicolas , Harvard Medical School
+
#Sudhir Pathak, Univeristy Of Pittsburgh
−
# Riklin Raviv Tammy , MIT, CSAIL
+
#Thierry PECOT, Ohio State University
−
# Ruiz Marco , UCSD
+
#Marta Peroni, Politecnico di Milano
−
# Schroeder William , Kitware
+
#Antonin Perrot-Audet, Harvard Medical School
−
# Scully Mark , The Mind Research Network
+
#Steve Pieper, Isomics, Inc.
−
# Sharp Greg , MGH
+
#Wendy Plesniak, Brigham and Women's Hospital
−
# Shi Yundi , UNC Chapel Hill
+
#Kilian Pohl, IBM
−
# Shusharina Nadya , MGH
+
#Sonia Pujol, Brigham and Women's Hospital
−
# Singh Shantanu , The Ohio State University
+
#Nicolas Rannou, Harvard Medical School
−
# Smith Gareth , Wolfson Medical Imaging Centre (WMIC)
+
#Tammy Riklin Raviv, MIT, CSAIL
−
# Souhait Lydie , Harvard Medical School
+
#Marco Ruiz, UCSD
−
# Spinczyk Dominik , Silesian University of Technology
+
#Johannes Schick, Surgical Planning Laboratory
−
# Srinivasan Padmapriya , BWH
+
#William Schroeder, Kitware, Inc.
−
# Tao Xiaodong , GE Research
+
#Mark Scully, The Mind Research Network
−
# Tokuda Junichi , Brigham and Women's Hospital
+
#Gunasekaran Seetharaman, US Air Force Research Lab
−
# Ungi Tamas , Queen's University
+
#Greg Sharp, MGH
−
# Vachet Clement , UNC Chapel Hill
+
#Yundi Shi, UNC Chapel Hill
−
# Veni Gopalkrishna , SCI Institute
+
#Nadya Shusharina, MGH
−
# Wassermann Demian , SPL/LMI/PNL
+
#Shantanu Singh, The Ohio State University
−
# Weinrich Adam , Nokia
+
#Gareth Smith, Wolfson Medical Imaging Centre (WMIC)
−
# Wells Sandy , BWH
+
#Lydie Souhait, Harvard Medical School
−
# White Phillip , BWH/HMS
+
#Dominik Spinczyk, Silesian University of Technology
−
# Wu Guorong , University of North Carolina at Chapel Hill
+
#Padmapriya Srinivasan,
−
# Yamada Atsushi , Nagoya Institute of Technology
+
#Xiaodong Tao, GE Research
−
# Yarmarkovich Alexander , ISOMICS
+
#Matthew Toews, Brigham and Women's Hospital
−
# Zaitsev Alexander , Brigham and Womens Hospital
+
#Junichi Tokuda, Brigham and Women's Hospital
 +
#Tamas Ungi, Queen's University
 +
#Clement Vachet, UNC Chapel Hill
 +
#Veda Vadyar, Brigham and Women's Hospital
 +
#Gopalkrishna Veni, SCI Institute
 +
#Stuart Wallace, Massachusetts General Hospital
 +
#Demian Wassermann, Surgical Planning Laboratory, LMI, PNL
 +
#Yihan Wei, Brigham and Women's Hospital
 +
#Adam Weinrich, Nokia
 +
#Sandy Wells, Brigham and Women's Hospital
 +
#Phillip White, Brigham and Women's Hospital
 +
#Guorong Wu, University of North Carolina at Chapel Hill
 +
#Yin Wu, Mass General Hospital
 +
#Atsushi Yamada, Nagoya Institute of Technology
 +
#Alexander Yarmarkovich, ISOMICS
 +
#Alexander Zaitsev, Brigham and Women's Hospital
 +
 
 +
Please make sure that you are on the [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week NA-MIC Project Week mailing list].

Latest revision as of 13:05, 30 June 2017

Home < 2010 Summer Project Week

Back to Events

PW-MIT2010.png

Welcome to the web page for the 11th Project Week!

Summary

The 11th PROJECT WEEK was held on June 21-25, 2010 in Boston, at MIT and Brigham and Women's Hospital. It recorded 126 registered attendees, who worked on 71 projects. These attendees represented 30 academic sites and 15 companies. Participants traveled to the project week from 9 countries (Austria, Singapore, France, Germany, Japan, Italy, England, Poland, and Canada), and from 16 states within the US (MA, NY, NC, MD, CA, UT, OH, MO, GA, PA, CO, IA, FL, DC, CT, NM). The projects, agenda, and affiliations of attendees are detailed below.

A summary of all past Project Events.

  • Volume Rendering Breakout Session

  • Raise Your Hand if you are a NRRD

  • Hard at Work

  • Brainlab VVlink OpenIGTLink Demo

  • Tutorial Contest Presentation

More Photos

Projects

Segmentation

  1. Robust Statistics Segmenter Slicer Module (Yi Gao, Allen Tannenbaum, Ron Kikinis)
  2. Multi-scale Shape Based Segmentation for the Hippocampus (Yi Gao, Allen Tannenbaum)
  3. Prostate Segmentation from MRI (Andriy Fedorov, Yi Gao)
  4. Segmentation on Mesh Surfaces Using Geometric Information (Peter Karasev, Karol Chudy, Allen Tannenbaum, GT; Ron Kikinis, BWH)
  5. SPECTRE: Skull Stripping Integration with Slicer (Nicole Aucoin, Min Chen)
  6. White Matter Lesion Segmentation (Minjeong Kim, Xiaodong Tao, Jim Miller, Dinggang Shen)
  7. EMSegmentation: Automatic Intensity Initialization using KMeans (Priya Srinivasan, Daniel Haehn, Kilian Pohl, Sylvain Bouix)
  8. LV Scar Segmentation Display and Fusion (Dana C. Peters, Felix Liu, BIDMC, Boston)
  9. The Vascular Modeling Toolkit in 3D Slicer (Daniel Haehn, Luca Antiga, Kilian Pohl, Johannes Schick, Steve Pieper, Ron Kikinis)

Registration

  1. The 3DSlicer Registration Case Library (Dominik Meier)
  2. Evaluation of Registration in Slicer (James Fishbaugh, Guido Gerig, Domink Meier)
  3. HAMMER: Deformable Registration (Guorong Wu, Xiaodong Tao, Jim Miller, Dinggang Shen)
  4. Best Regularization Term for Demons Registration Algorithm (Rui Li, Greg Sharp)
  5. Fiducial-based Deformable Image Registration (Nadya Shusharina, Greg Sharp)
  6. MR to Ultrasound Registration Methodology (Dieter Hahn, William Wells, Joachim Hornegger, Tina Kapur, Stephen Aylward, Andriy Fedorov)
  7. Groupwise Registration (Ryan Eckbo, Sylvain Bouix, Jim Miller, Hans Johnson, Kilian Pohl, Daniel Haehn)

Shape Analysis

  1. Shape Test Bench (Marc Niethammer, Sylvain Bouix)
  2. Median Shape by Boundary-based Distance (Tammy Riklin Raviv, Sylvain Bouix)
  3. Shape Analysis Projects, Integration with Slicer3 (Beatriz Paniagua, Martin Styner)
  4. Particle Based Shape Regression (Manasi Datar, Joshua Cates, P. Thomas Fletcher, Sylvain Gouttard, Guido Gerig, Ross Whitaker)
  5. Automatic SPHARM Shape Analysis in 3D Slicer (Corentin Hamel, Clement Vachet, Beatriz Paniagua, Nicolas Augier, Martin Styner)

Diffusion

  1. NAMIC Tools Suite for DTI Analysis (Hans Johnson, Joy Matsui, Vincent Magnotta, Sylvain Gouttard)
  2. Implementing Two-tensor Tractography in Slicer (Python) (Stefan Leinhard, James Malcolm, Demian Wasserman, C-F Westin, Yogesh Rathi)
  3. Efficient Diffusion Connectivity via Multi­directional F­star (Alexis Boucharin, Clement Vachet, Yundi Shi, Mar Sanchez, Martin Styner)
  4. Fluid Mechanics Based Tractography (Nathan Hageman)
  5. QSpace Imaging Reconstruction for Diffusion Spectrum Imaging Data (Sudhir Pathak)

IGT

  1. MR to CT Registration for Prostate Brachytherapy Dose Calculation (Andriy Fedorov, Dominik Meier, Hans Johnson)
  2. Intraoprative Brain Shift Monitoring using Shear Mode Transcranial Ultrasound (Jason White, Steve Pieper, Junichi Tokuda, Pratik Patel?)
  3. Prostate Intervention(Junichi Tokuda, Tamas Ungi, Haiying Liu, Sam Song)
  4. Liver Ablation (Haiying Liu, Noby Hata)
  5. BrainLab-Aurora Hybrid Navigation (Isaiah Norton, Dan Marcus, Noby Hata)
  6. PerkStation Module (Tamas Ungi, Xiaodong Tao)
  7. Co-registration of PET and DWI Images for Targeting Glioma Biopsies (Gareth Smith, Dominik Meir, Vince Magnotta)
  8. Implementing Open IGT Link to Virtual Place for Research Support (Nicholas Herlambang, Masakatsu Hoashi, Junichi Tokuda, Noby Hata)
  9. Tracking Neuroendoscope using EM Tracker and OpenIGTLink (Laurent Chauvin, Junichi Tokuda, Noby Hata)
  10. Implementing OpenCV to Slicer3 for Neuroendoscopic Surgery (Atsushi Yamada, Junichi Tokuda, Noby Hata)

Radiotherapy

  1. Dicom RT Plugin (Greg Sharp, Tamas Ungi)
  2. Adaptive Radiation Therapy for H&N Cancer (Marta Peroni,Polina Golland,Greg Sharp)
  3. Segmentation for Adaptive Radiotherapy for Head, Neck, and Thorax (Ivan Kolesov, Greg Sharp, and Allen Tannenbaum )

Analysis

  1. IA-FEMesh Slicer3 Finite Meshing Module (N Grosland, V Magnotta, C Lisle, S Pieper)
  2. Cortical Thickness Analysis (Clement Vachet, Heather Cody Hazlett, Martin Styner)
  3. Mouse Brain Cortical Thickness Analysis (Joohwi Lee, Ipek Oguz, Martin Styner)
  4. Primate Image Analysis using the Standard Slicer Pipeline (Yundi Shi, Martin Styner, Clement Vache, Mar Sanchez, Andriy Fedorov)
  5. MRSI Module and SIVIC Interface (B Menze, M Phothilimthana, J Crane (UCSF), B Olson (UCSF), P Golland)
  6. Femoral Fracture Classification Brainstorming Session (Karl Fritscher, Vince Magnotta, Peter Karasev, Curt Lisle, Ron Kikinis)
  7. Computer Aided Photodynamic Therapy (E Pietka, D Spinczyk, P Szabelak)
  8. Quantification of Lesion Diffusion Disruption (M Scully, H J Bockholt)
  9. Lupus Lesion Segmentation and Review Statistics (M Scully, H J Bockholt)

Microscopy Image Analysis

  1. DICOM supplement 145  : Microscopy Image in the Dicom Standard (Mathieu Malaterre, Alex. Gouaillard)
  2. Microscopy Extensions for ITK: Convolution, Deconvolution, Wavelets and More ( Gaetan Lemhann, Alex. Gouaillard )
  3. Import/Export Farsight - GoFigure Results (Arnaud Gelas, Lydie Souhait, Kedar Grama, Raghav Padmanabhan, Sean Megason, Badri Roysam)
  4. JPEG2000 and HDF5 Image Readers in ITK (Kishore Mosaliganti, Luis Ibanez, Sean Megason)
  5. ITK Spherical Harmonics Filter for Shape Analysis of Cell Nuclei (Shantanu Singh, Kishore Mosaliganti, Arnaud Gelas, Sean Megason, Raghu Machiraju)
  6. ITK Analysis of Large Histology Datasets (Liya Ding, Kun Huang, Sean Megason, Raghu Machiraju)
  7. CTK Transfer Function Widget (Nicolas Rannou, Julien Finet, Arnaud Gelas, Stever Pieper)
  8. Seedings Results Comparison (Antonin Perrot-Audet, Raghav Padmanabhan, Kishore Mosaliganti, Badri Roysam, Sean Megason)
  9. ITK Multiphase and GPAC Level Sets (K. Palaniappan, Ilker Ersoy, Filiz Bunyak, Kishore Mosaliganti, Sean Megason)
  10. Median Binary Pattern Texture Measures for Cell Nuclei Segmentation (Adel Hafiane, Lucas Menand, K. Palaniappan, Sean Megason)
  11. Standards and Interfaces for Microscopy Image Analysis in ITK (whoever has an opinion, Sean Megason)

NA-MIC Kit Internals

  1. Module Inventory (Steve, Jim)
  2. Viewer Manager Factory (Alex Yarmarkovich, Kilian, Steve, Nicole)
  3. Programmatic use of Volume Rendering Module (Andriy Fedorov, Yanling Liu, Alex Yarmarkovich, Jim Barabas, Johannes Schick)
  4. Inventory of Volume Rendering Functionality (Jim Barabas, Noby Hata)
  5. Consistent Visual Language for Slicer4: Icon Rework Marathon (Wendy Plesniak)
  6. Slicer Wizard for PET/CT Workflow (Wendy Plesniak, Ron Kikinis, Alexander Zaitsev)
  7. PythonQt and Console Widget (Steve Pieper, Jean-Christophe Fillion-Robin)
  8. VTKWidgets (Jean-Christophe Fillion-Robin, Will Schroeder, Nicole Aucoin, Wendy, Ron Kikinis)
  9. Superbuild (David Partyka, Steve Pieper, Katie Hayes)
  10. Paraview Support for Computational Anatomy (Michel Audette, Mike Bowers)
  11. Real-Time Volume Rendering for Virtual Colonoscopy (Hiro Yoshida, Yin Wu, Steve Pieper, Ron Kikinis)

Workflows and Integration

  1. Workflows and Service Oriented Architecture Solutions for Slicer3 Modules (Alexander Zaitsev, Wendy Plesniak, Charles Guttmann, Ron Kikinis)

Agenda

Time Monday, June 21 Tuesday, June 22 Wednesday, June 23 Thursday, June 24 Friday, June 25
Project Presentations NA-MIC Update Day IGT Day Reporting Day
8:30am Breakfast Breakfast Breakfast Breakfast
9am-12pm 9am: NA-MIC Kit Update (Jim Miller)

Grier Rooms
----------------------------------------
9:20am: 3D Slicer Update (Steve Pieper)
Grier Rooms
----------------------------------------
10am: Superbuild Demo (Dave Partyka)
Grier Rooms
----------------------------------------
10:15am: Break
Grier Rooms
----------------------------------------
10:30-11am: OpenIGTLink Update (Junichi Tokuda)
Grier Rooms
----------------------------------------
11am-12pm: Slicer Hands-on Workshop (Randy Gollub, Sonia Pujol)
Star Room

9am-12pm: Breakout Session:
ITK (Luis Ibanez)


Star Room

9am-5pm: Breakout Session:
OpenIGTLink


Grier Rooms

10am-12pm: Project Progress Updates


Grier Rooms

12pm-1pm Lunch Lunch Lunch Lunch Lunch boxes; Adjourn by 1:30pm
1pm-5:30pm 1-1:05pm: Ron Kikinis: Welcome

Grier Rooms
----------------------------------------
1:05-3:30pm: Project Introductions (all Project Leads)
Grier Rooms
----------------------------------------
3:30-5:30pm: Tutorial: Getting Started with Qt (Adam Weinrich, Nokia)
32-155 (Stata Lecture Hall)

1-3pm: Breakout Session:
QT/Slicer (Steve, JC, J2)


Star Room
----------------------------------------
3-4pm: Tutorial Contest Presentations
Grier Rooms
----------------------------------------
4-5pm: Breakout Session:
Data Management (Stephen Aylward)
Star Room

12:45-1pm: Tutorial Contest Winner Announcement


Grier Rooms
----------------------------------------
1-3pm: Breakout Session:
Microscopy Image Analysis (Sean Megason)
Kiva Room
----------------------------------------
3-5pm: Breakout Session:
QA Training (Luis Ibanez)
Star Room
----------------------------------------
3-4pm: Breakout Session:
VTK Widgets (Nicole, Kilian, JC)
32-261 Room
----------------------------------------

5pm: Reception

R&D Pub

1-2pm: Breakout Session:
GWE (Marco Ruiz)


----------------------------------------
2-3pm: Simple Git (Steve Pieper) (Slides)
----------------------------------------
3-4pm: Breakout Session:
Volume Rendering Demos and Discussion (Yin Wu, Steve Pieper)

5:30pm Adjourn for the day Adjourn for the day Adjourn for the day Adjourn for the day

Please note:

Background

We are pleased to announce the 11th PROJECT WEEK of hands-on research and development activity for applications in Image-Guided Therapy, Neuroscience, and several additional areas of biomedical research that enable personalized medicine. Participants will engage in open source programming using the NA-MIC Kit, algorithm design, medical imaging sequence development, tracking experiments, and clinical application. The main goal of this event is to move forward the translational research deliverables of the sponsoring centers and their collaborators. Active and potential collaborators are encouraged and welcome to attend this event. This event will be set up to maximize informal interaction between participants.

Active preparation begins on Thursday, April 15th at 3pm ET, with a kick-off teleconference. Invitations to this call will be sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties who have expressed an interest in working with these centers. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient coverage for all. Subsequent teleconferences will allow for more focused discussions on individual projects and allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading up to the meeting, all project teams will be asked to fill in a template page on this wiki that describes the objectives and plan of their projects.

The event itself will start off with a short presentation by each project team, driven using their previously created description, and will help all participants get acquainted with others who are doing similar work. In the rest of the week, about half the time will be spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half will be spent in project teams, doing hands-on project work. The hands-on activities will be done in 30-50 small teams of size 2-4, each with a mix of multi-disciplinary expertise. To facilitate this work, a large room at MIT will be setup with several tables, with internet and power access, and each computer software development based team will gather on a table with their individual laptops, connect to the internet to download their software and data, and be able to work on their projects. Teams working on projects that require the use of medical devices will proceed to Brigham and Women's Hospital and carry out their experiments there. On the last day of the event, a closing presentation session will be held in which each project team will present a summary of what they accomplished during the week.

This event is part of the translational research efforts of NA-MIC, NCIGT, NAC, Harvard Catalyst, and CIMIT. It is an expansion of the NA-MIC Summer Project Week that has been held annually since 2005. It will be held every summer at MIT and Brigham and Women's Hospital in Boston, typically during the last full week of June, and in Salt Lake City in the winter, typically during the second week of January.

Logistics

  • Dates: June 21-25, 2010
  • Location: MIT. Grier Rooms A & B: 34-401A & 34-401B.
  • REGISTRATION: Please click here to do an on-line registration for the meeting that will allow you to pay by credit card, or send a check.
  • Registration Fee: $260 (covers the cost of breakfast, lunch and coffee breaks for the week).
  • Hotel: We have reserved a block of rooms at the Boston Marriott Cambridge Hotel, Two Cambridge Center, 50 Broadway, Cambridge, MA 02142. (Phone: 617.252.4405, Fax: 617.494.6565) Please click here to reserve. You will be directed to the property's home page with the group code already entered in the appropriate field. All you need to do is enter your arrival date to begin the reservation process.
  • All reservations must be made by Tuesday, June 1, 2010 to receive the discounted rate of
  • $189/night/room (plus tax).
  • This rate is good only through June 1, 2010.

Please note that if you try to reserve a room outside of the block on the shoulder nights via the link, you will be told that the group rate is not available for the duration of your stay. To reserve those rooms, which might not be at the group rate because it is based upon availability, please call Marriott Central Reservations at 1-800-228-9290.

  • Here is some information about several other Boston area hotels that are convenient to NA-MIC events: Boston_Hotels. Summer is tourist season in Boston, so please book your rooms early.
  • For hosting projects, we are planning to make use of the NITRC resources. See Information about NITRC Collaboration


Preparation

  1. Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
  2. The NA-MIC engineering team will be discussing infrastructure projects in a kickoff TCON on April 15, 3pm ET. In the weeks following, new and old participants from the above mailing list will be invited to join to discuss their projects, so please make sure you are on it!
  3. By 3pm ET on June 10, 2009: Complete a templated wiki page for your project. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
  4. By 3pm on June 17, 2010: Create a directory for each project on the NAMIC Sandbox (Zack)
    1. Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
    2. Gather test images in any of the Data sharing resources we have (e.g. XNAT/MIDAS). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
    3. Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)
  5. Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...
  6. People doing Slicer related projects should come to project week with slicer built on your laptop.
    1. Projects to develop extension modules should work with the Slicer-3-6 branch (new code should not be checked into the branch).
    2. Projects to modify core behavior of slicer should be done on the trunk.

Attendee List

NOTE: THIS IS AN AUTOMATICALLY GENERATED LIST FROM THE REGISTRATION WEBSITE. ATTENDEES SHOULD NOT EDIT THIS, BUT REGISTER BY CLICKING HERE.

  1. Yousef Al-Kofahi, CompuCyte Corporation
  2. Peter Anderson, retired
  3. Nicole Aucoin, Brigham and Women's Hospitall
  4. Michel Audette, Kitware, Inc.
  5. Stephen Aylward, Kitware, Inc.
  6. Jim Barabas, MIT
  7. Barrett Ryan, Brigham and Women's Hospital
  8. Alexis Boucharin, UNC Neuro Image Research and Analysis Laboratories
  9. Sylvain Bouix, Brigham and Women's Hospital
  10. Michael Bowers, Johns Hopkins University
  11. Francois Budin, UNC
  12. Everette Burdette, Acoustic MedSystems, Inc.
  13. Laurent Chauvin, Brigham and Women's Hospital
  14. Min Chen, Johns Hopkins University
  15. Jason Crane, UCSF
  16. Nikos Chrisochoides, College of William and Mary
  17. Manasi Datar, SCI Institute
  18. Liya Ding, The Ohio State University
  19. Ryan Eckbo, Brigham and Women's Hospital
  20. Ilker Ersoy, University of Missouri Columbia
  21. Andriy Fedorov, Surgical Planning Lab
  22. Jean-Christophe Fillion-Robin, Kitware, Inc.
  23. Julien Finet, Kitware, Inc.
  24. James Fishbaugh, SCI Institute
  25. Karl Fritscher, UMIT
  26. Yi Gao, Gerogia Tech
  27. Arnaud GELAS, Harvard Medical School
  28. Randy Gollub, MGH
  29. Chris Gorgolewski, Surgical Planning Laboratory
  30. alexandre gouaillard, CoSMo Software
  31. Sylvain Gouttard, SCI Institute
  32. Kedar Grama, Rensselaer Polytechnic Institute
  33. Daniel Haehn, University of Pennsylvania
  34. Adel Hafiane, ENSI-Bourges
  35. Nathan Hageman,
  36. Dieter Hahn, University of Erlangen
  37. Michael Halle, Surgical Planning Laboratory, Brigham and Women's Hospital
  38. Corentin Hamel, UNC Chapel Hill
  39. Nobuhiko Hata, Brigham and Women's Hospital
  40. Kathryn Hayes, Brigham and Women's Hospital
  41. Nicholas Herlambang, AZE, Ltd.
  42. Masakatsu Hoashi, AZE Ltd.
  43. Leslie Holton, Medtronic Navigation
  44. Luis Ibanez, Kitware, Inc.
  45. Jayender Jagadeesan, Surgical Planning Laboratory, Brigham and Women's Hospital
  46. Hans Johnson, University of Iowa
  47. Tina Kapur, Brigham and Women's Hospital
  48. Peter Karasev, Georgia Tech
  49. Ron Kikinis, Brigham and Women's Hospital
  50. Minjeong Kim, UNC-Chapel Hill
  51. Ivan Kolesov, Georgia Institute of Technology
  52. Garrett Larson, UNC-CH
  53. Joohwi Lee, UNC Chapel Hill
  54. Rui Li, MGH
  55. Stefan Lienhard, LMI
  56. Curtis Lisle, KnowledgeVis, LLC
  57. Haiying Liu, Brigham and Women's Hospital
  58. Felix Liu, Beth Israel Deaconess Medical Center
  59. Yanling Liu, SAIC-Frederick, Inc.
  60. Bradley Lowekamp, Lockheed Martin
  61. Raghu Machiraju, The Ohio State University
  62. Vincent Magnotta, The University of Iowa
  63. Mathieu Malaterre, CoSMo Software
  64. Charles Maneval, Brigham and Women's Hospital
  65. Daniel Marcus, Washington University
  66. William Marks, Focused Ultrasound Lab, Brigham and Women's Hospital
  67. Katie Mastrogiacomo, Brigham and Women's Hospital
  68. Joy Matsui, University of Iowa
  69. Sean Megason, Harvard Medical School
  70. Dominik Meier, Brigham and Women's Hospital
  71. Bjoern Menze, CSAIL MIT
  72. Mikhail Milchenko, WUSTL
  73. James Miller, GE Research
  74. Kishore Mosaliganti, Harvard Medical School
  75. Marc Niethammer, UNC Chapel Hill
  76. Isaiah Norton, Brigham and Women's Hospital
  77. Beck Olson, UCSF
  78. John Onofrey, Yale University
  79. Raghav Padmanabhan, RPI
  80. Kannappan Palaniappan, University of Missouri
  81. Beatriz Paniagua, University of North Carolina at Chapel Hill
  82. Xenophon Papademetris, Yale University
  83. Eun-Joo Park, Brigham and Women's Hospital
  84. David Partyka, Kitware, Inc.
  85. Pratik Patel,
  86. Sudhir Pathak, Univeristy Of Pittsburgh
  87. Thierry PECOT, Ohio State University
  88. Marta Peroni, Politecnico di Milano
  89. Antonin Perrot-Audet, Harvard Medical School
  90. Steve Pieper, Isomics, Inc.
  91. Wendy Plesniak, Brigham and Women's Hospital
  92. Kilian Pohl, IBM
  93. Sonia Pujol, Brigham and Women's Hospital
  94. Nicolas Rannou, Harvard Medical School
  95. Tammy Riklin Raviv, MIT, CSAIL
  96. Marco Ruiz, UCSD
  97. Johannes Schick, Surgical Planning Laboratory
  98. William Schroeder, Kitware, Inc.
  99. Mark Scully, The Mind Research Network
  100. Gunasekaran Seetharaman, US Air Force Research Lab
  101. Greg Sharp, MGH
  102. Yundi Shi, UNC Chapel Hill
  103. Nadya Shusharina, MGH
  104. Shantanu Singh, The Ohio State University
  105. Gareth Smith, Wolfson Medical Imaging Centre (WMIC)
  106. Lydie Souhait, Harvard Medical School
  107. Dominik Spinczyk, Silesian University of Technology
  108. Padmapriya Srinivasan,
  109. Xiaodong Tao, GE Research
  110. Matthew Toews, Brigham and Women's Hospital
  111. Junichi Tokuda, Brigham and Women's Hospital
  112. Tamas Ungi, Queen's University
  113. Clement Vachet, UNC Chapel Hill
  114. Veda Vadyar, Brigham and Women's Hospital
  115. Gopalkrishna Veni, SCI Institute
  116. Stuart Wallace, Massachusetts General Hospital
  117. Demian Wassermann, Surgical Planning Laboratory, LMI, PNL
  118. Yihan Wei, Brigham and Women's Hospital
  119. Adam Weinrich, Nokia
  120. Sandy Wells, Brigham and Women's Hospital
  121. Phillip White, Brigham and Women's Hospital
  122. Guorong Wu, University of North Carolina at Chapel Hill
  123. Yin Wu, Mass General Hospital
  124. Atsushi Yamada, Nagoya Institute of Technology
  125. Alexander Yarmarkovich, ISOMICS
  126. Alexander Zaitsev, Brigham and Women's Hospital

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